LOCUS       NC_020251               5262 bp    DNA     circular CON 04-MAY-2024
DEFINITION  Shigella sonnei plasmid pDPT2, complete sequence.
ACCESSION   NC_020251
VERSION     NC_020251.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14229330
KEYWORDS    RefSeq; complete replicon.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1
  AUTHORS   Holt,K.E., Thieu Nga,T.V., Thanh,D.P., Vinh,H., Kim,D.W., Vu
            Tra,M.P., Campbell,J.I., Hoang,N.V., Vinh,N.T., Minh,P.V.,
            Thuy,C.T., Nga,T.T., Thompson,C., Dung,T.T., Nhu,N.T., Vinh,P.V.,
            Tuyet,P.T., Phuc,H.L., Lien,N.T., Phu,B.D., Ai,N.T., Tien,N.M.,
            Dong,N., Parry,C.M., Hien,T.T., Farrar,J.J., Parkhill,J., Dougan,G.,
            Thomson,N.R. and Baker,S.
  TITLE     Tracking the establishment of local endemic populations of an
            emergent enteric pathogen
  JOURNAL   Proc Natl Acad Sci U S A 110 (43), 17522-17527 (2013)
   PUBMED   24082120
REFERENCE   2  (bases 1 to 5262)
  AUTHORS   Duy,P.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-DEC-2012) Enterics Infection, Oxford University
            Clinical Research Unit, 156/7N To Hien Thanh Dis10, HCMC, 084, VIET
            NAM
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_009955805.2-RS_2024_05_04
            Annotation Date                   :: 05/04/2024 05:35:23
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 11
            CDSs (total)                      :: 11
            Genes (coding)                    :: 10
            CDSs (with protein)               :: 10
            Genes (RNA)                       :: 0
            tRNAs                             :: 0
            ncRNAs                            :: 0
            Pseudo Genes (total)              :: 1
            CDSs (without protein)            :: 1
            Pseudo Genes (ambiguous residues) :: 0 of 1
            Pseudo Genes (frameshifted)       :: 0 of 1
            Pseudo Genes (incomplete)         :: 1 of 1
            Pseudo Genes (internal stop)      :: 0 of 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            HF565445.2.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..5262
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="EG211"
                     /db_xref="taxon:624"
                     /plasmid="pDPT2"
                     /note="clinical isolate"
     gene            414..527
                     /locus_tag="HXG54_RS00055"
     CDS             414..527
                     /locus_tag="HXG54_RS00055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001427889.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGN"
                     /name="hypothetical protein"
     gene            933..1322
                     /locus_tag="HXG54_RS00005"
                     /old_locus_tag="ST624_p2"
     CDS             933..1322
                     /locus_tag="HXG54_RS00005"
                     /old_locus_tag="ST624_p2"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679965.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000477210.1"
                     /translation="MFKSSVKSITSSTILTLLIGCSSTETNKNIVYKVGGDSIILNKYC
                     ILKMYPSQSEKNKGVIIEVNTDSLCKKKLNEITSKNIGKPLISYFDGKVISQPAIIHSA
                     LNPTHYYQPVNDETTVMEIIKAYSK"
                     /name="hypothetical protein"
     gene            complement(1386..1670)
                     /locus_tag="HXG54_RS00010"
                     /old_locus_tag="ST624_p3"
     CDS             complement(1386..1670)
                     /locus_tag="HXG54_RS00010"
                     /old_locus_tag="ST624_p3"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000625497.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin Z C-terminal domain-related protein"
                     /protein_id="WP_000625497.1"
                     /translation="MISQNVWAPPFFFGPWVELENHTGDIAYTVYFDTLSNVPGPFIAF
                     IWYAPNGPRTVNVIGPASYQISCKGAGVDKIKFKSVSGTGQIIHVYTTL"
                     /name="colicin Z C-terminal domain-related protein"
     gene            complement(1688..1885)
                     /locus_tag="HXG54_RS00015"
                     /old_locus_tag="ST624_p1"
     CDS             complement(1688..1885)
                     /locus_tag="HXG54_RS00015"
                     /old_locus_tag="ST624_p1"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335786.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001335786.1"
                     /translation="MKEEKVLLHRFLFVVRNKNGCELSCSADLMGTRDDVYKYFSDSVS
                     GLDVELIDVSCESEWEEHSH"
                     /name="hypothetical protein"
     gene            2097..2393
                     /locus_tag="HXG54_RS00020"
                     /old_locus_tag="ST624_p4"
     CDS             2097..2393
                     /locus_tag="HXG54_RS00020"
                     /old_locus_tag="ST624_p4"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_015386304.1"
                     /translation="MSKTKSGRHRLSKTDKRLLAALIAAGYEERTARDLIQKHVYTLTQ
                     ADLRHLVSEISNGVGQSQAYDAIYQARRIRLARKLLNGKKPEEGLNAWKGDLP"
                     /name="hypothetical protein"
     gene            complement(2938..3171)
                     /locus_tag="HXG54_RS00025"
                     /old_locus_tag="ST624_p6"
     CDS             complement(2938..3171)
                     /locus_tag="HXG54_RS00025"
                     /old_locus_tag="ST624_p6"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137439.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3178..3708)
                     /locus_tag="HXG54_RS00030"
                     /old_locus_tag="ST624_p7"
     CDS             complement(3178..3708)
                     /locus_tag="HXG54_RS00030"
                     /old_locus_tag="ST624_p7"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_015386306.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETILNDEFRKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGMIQANLEEIRKQNENLEKLNAKTWGVRYHEGSNGRFLVLPEGMKAETNWTM
                     ENGKQNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(<3746..4408)
                     /locus_tag="HXG54_RS00050"
                     /pseudo=""
     CDS             complement(<3746..4408)
                     /locus_tag="HXG54_RS00050"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(4386..4709)
                     /locus_tag="HXG54_RS00040"
                     /old_locus_tag="ST624_p8"
     CDS             complement(4386..4709)
                     /locus_tag="HXG54_RS00040"
                     /old_locus_tag="ST624_p8"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_176703062.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVAXXGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4774..4965
                     /locus_tag="HXG54_RS00045"
                     /old_locus_tag="ST624_p9"
     CDS             4774..4965
                     /locus_tag="HXG54_RS00045"
                     /old_locus_tag="ST624_p9"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(5051..5230)
                     /locus_tag="HXG54_RS00060"
     CDS             complement(5051..5230)
                     /locus_tag="HXG54_RS00060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447730.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024195267.1"
                     /translation="MSEEAEKRLDVHFLLTHLCGISHPVWRTFHTIRTDAAWLSQYTLR
                     YRYVTGSGLRPDTR"
                     /name="hypothetical protein"
     Typing          complement(5051..5137)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="2.47e-38"
     Typing          2..486
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.177"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2835..4396)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcctcgctca ctgactcgct acgctcggtc gttcgactgc ggcgagcggt atctactcac
       61 tcaaaaacga aatgctgtta tccacagaat caggggataa caccggaaaa aacatgtgag
      121 caaaagacca ggaacaggaa gaaggccgcg ccgctggcgt ttttccatag gctccgcccc
      181 cctgacgagc atcacaaaaa cagatgctca agtcagaggt ggcgaaaccc gacaggactt
      241 aaagatacca ggcgtttccc cccggaagct ccctcgtgcg ctctcctgtt ccgaccttac
      301 cgtttaccgg atacctgtcc gcctttctcc cttcgggaag cgtggcgctt tctcatagct
      361 cacgctgtag gtatctcagt tcggtgtagg tcgttcgctc caagctgggc tgtgtgcacg
      421 aaccccccgt tcagcccgac cgctgcgcct tatccggtaa ctatcgtctt gagtccaacc
      481 cggtaagaca cgacttaacg ccactggcag cagccattgg taactaaaaa gtggatttag
      541 atacgcagaa ctcttgaagt tgaagcctta tagcggctac actgaaagga catcttttgg
      601 tatctgtgct ccacttaagc cagctacccg gttaggtaat ctgccaggat tagctaacct
      661 tcgaaaaacc acctgccagg gtggtttttt cgtttacagg cagcagatta cgcgcagaaa
      721 aaaaggatct caagaagatc ctttgatctt ttttctctaa actgcaatcc catcagttca
      781 ggagagaaag atagtataat tgccctctct tatatggaac caccattcaa tcacatcatg
      841 ggaataatat aagtgaaaac gttcgcattg tttattttta cgtgtatatg tatttataga
      901 ttggaatttt aacaaaataa aatggagtta atatgttcaa atcatcagta aagtcaataa
      961 catcgagtac tatactgacc ttacttatag gatgttcaag tactgaaaca aacaaaaaca
     1021 ttgtttacaa agttggtggt gacagcatca ttctgaataa atattgcata cttaaaatgt
     1081 acccttccca atcagaaaaa aacaaaggcg tcataataga agtaaacaca gatagtttat
     1141 gtaagaaaaa actaaacgaa ataactagta aaaatatagg gaaacccctg atttcatatt
     1201 ttgatggaaa agtaatatcc caacctgcaa tcattcattc tgcactaaat ccaacccatt
     1261 attatcaacc tgtgaacgat gaaacaacag tgatggaaat cataaaagca tattcaaaat
     1321 aatattaata gatataatcc tgcttaaggt atagcttagg caggattata tctattcagc
     1381 tcttattata aggtagtgta tacatgaata atctgccctg tcccactgac acttttaaat
     1441 ttaattttat caacaccagc gcccttgcaa gagatctgat aagatgctgg accaataacg
     1501 ttaactgttc ttggcccatt aggggcatac cagataaaag caataaatgg accgggtaca
     1561 ttagacaatg tatcaaaata gacagtgtac gcgatatcac cagtatgatt ttcaagttca
     1621 acccaaggac caaaaaagaa aggaggagcc caaacatttt gagaaatcat ataatctcct
     1681 gattagttca atgcgaatgt tcttcccatt cactctcgca agaaacatct ataagctcaa
     1741 catctagccc actaacagaa tcagagaaat acttataaac atcatccctt gttcccataa
     1801 ggtctgccga acatgatagt tcacaaccat tcttattcct aactacaaat aagaaacggt
     1861 gaagcaatac tttttcttct ttcattttat ccctcccttt atttacacag aatatactgt
     1921 atatataaat actagtttta tatacagtat aaattacgcc gcattatttt tcctgtcaat
     1981 gatatgaatt ttcatttttg tgatctgaat cacccttata aaaatcagga agggaagatt
     2041 cgcagcagaa aaacagcacc ggataacatc aagagaaaaa acagagagga gataacgtga
     2101 gcaaaacaaa atctggtcgc caccgactga gcaaaacaga caaacgcctg ctggctgcac
     2161 ttatcgctgc cggatacgaa gagcggacag cccgtgacct catccagaaa cacgtttaca
     2221 cactgacaca ggccgacctg cgccatctgg tcagtgaaat cagtaacggt gtgggacagt
     2281 cacaggccta cgatgcgatt taccaggcaa gacgcattcg tctcgcccgt aaactcctga
     2341 acggaaaaaa accggaagaa gggctgaacg cctggaaggg tgatttacca taatcactta
     2401 ttgtacgcac cgctgaaacg cgttcggcgc gatcacggca gcagacaggt aaaaatggca
     2461 acaaaccacc cgaaaaactg ccgcgatcgt acccggtaaa ttttaaccac atgcatagct
     2521 atgcagctat gtgaatcatg caggaattgc cagccagaga cagctgaaac ggattttttt
     2581 catgctttcg gaagcgaaga agacggggac cggagcggga aaacagaagt tcaggggaat
     2641 gagcgcgatc tggcaataga ggcaaaacac agcaacaaaa gacacaccag aatcgcgccc
     2701 gtatgcgttt taacgcgttc ctgtgttttc agcaaggtct gactgaagcg cgttcccggt
     2761 gcccccgaac caaccattat cccaaaaaat gcaccggaaa cgcgctgaca acattttagc
     2821 ctgtctctga ttaccatccc agcgaagggc catccagtgt ccgttcctgt atttccagct
     2881 ggcgctcacg ctccagggat aacgcatgtt cgcgttcctg tatcagccgt tcgtccctta
     2941 tctcctgttc tcgctgtata actggctcaa gcgttctgtc tgctcgctca agtgctgcac
     3001 ctgctgactc aactgcatga cccgctcgtt cagcatcgcg ttgtcccgtt gcgtaagcga
     3061 aaacattttc tgcaattcca cgaaggcgct ctcccattcg ttcagccgct gcatatagtc
     3121 ctgttgcagt tgctctaatg cgttcagcaa atgtctttcc agctccgtca tgctctgtta
     3181 ctcctgtacc agccttacgg cattctgttt cccgttttcc atcgtccagt tcgtttcggc
     3241 tttcatcccc tcgggcaaca ccagaaaacg tccgttgctc ccctcgtgat aacgcacgcc
     3301 ccatgtcttc gcgttcagct tctccagatt ctcgttctgc ttcctgattt cttccaggtt
     3361 cgcctgtatc atcccgccaa gataccagag cgtcccgcca ctcacggtaa acaggaaaat
     3421 gaccatcccc agtaacatca tgcccgtatt ccctgccagc tttaacacgt ccttcctgtg
     3481 ctgcatcatc gcctctttca ccccttcccg gtgttttttc agtgattcct ctgtcgaagc
     3541 tgtgaacagg gctatagcgt ctttgatttt cgtctcgttt gatgtcacag ccttgcttac
     3601 agatttttcg agcttcctga actcgtcgtt cagtattgtc tctgtagatt cggctctctc
     3661 tttcagcttt ttctcgaact ccgcgcccgt ctgtaaaaga ttgctcataa aatgctcctt
     3721 tcagcctgat attcttccca ccgttcgggt ctgcaatgct gatactgctt cgcgtcaccc
     3781 tgaccacttc aagccctgcc tctgtgagcg cctgaatcac atcctgacgg ccttttatct
     3841 ccccgacatg ataaagagcg tctatcccgc gtgtgacgct ctctgcaagc gcctgtttcg
     3901 tttccggcag gttatcaggg agagtcagta tccggcggtt ctccggggcg ttggggtcat
     3961 gcagcccgta atggtgatta accagcgtct gccaggcatc aattctcggc ctgtctgccc
     4021 ggtcgtagta cggctggagg cgttttccgc tctgtagctc catgttcgga atgacaaaat
     4081 tcagctcaag ccgtcccttg tcctggtgct ccacccacag gatgctgtac tgattttttt
     4141 cgagaccggg catcagtaca cgctcaaagc tcgccatcac cttttcacgt cctcccggcg
     4201 gcagctcctt ctccgcgaac gacagaacac ctgacgtgta tttcttcgca aatggcgtgg
     4261 catcgatgag ttcccggact tcttccggat taccctgaag caccgttgcc ccttcccggt
     4321 tacgctccct tcccagcagg taatcaaccg gaccactgcc accgcctttt cccctggcat
     4381 gaaacttaac tatcatcccg cgctccatgt tccctgacga cctgccgtaa gctgcgcaac
     4441 tctctctcga tggccatcag tgcggccacc acctgaaccc ggtcaccgga agaccactgc
     4501 ccgctgttca ccttcctcgc cgtctgattc aggttattcc cgatggcagc cagctggcgc
     4561 agtaacggcg gtgccagtgt cggcagcttc ccggnnnggg caaccggctc acccagacag
     4621 acccgccgca tccataccgc cagctgttta ccctcacagc gttcaagtaa ccgggcatgt
     4681 tcatcatcag taacccgtat tgtgagcatc ctctcgcgtt tcatcggtat cattatcccc
     4741 atgaacagaa atccccctta cacggaggca tcagtgacca aacaggaaaa aaccgccctt
     4801 aacatggccc gctttataag aagccagaca ttaacgctgc tggagaagct caacgaactg
     4861 gacgcggatg aacaggcaga tatctgtgaa tcgcttcacg accacgccga tgagctttac
     4921 cgcagttgcc tcgctcgctt cggggatgac ggtgaaaacc tctgacacat gcagctcccg
     4981 gagacggtca cagcttgtct gtgagcggat gccgggagct gacaagcccg tcagggcacg
     5041 tcagcgggtt ttagcgggtg tcggggcgca gccctgaccc agtcacgtag cgatagcgga
     5101 gtgtatactg gcttaaccat gcggcatcag tgcggatggt atgaaaagtg cgccataccg
     5161 ggtgtgaaat gccgcacaga tgcgtaagga gaaaatgcac gtccagccgc ttttccgctt
     5221 cctcgctcac tgactcgcta cgctcggtcg ttcgactgcg gc
//
